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- EMDB-40569: Cryo-EM structure of DDM1-HELLS chimera bound to the nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-40569
TitleCryo-EM structure of DDM1-HELLS chimera bound to the nucleosome
Map dataNon-sharpened cryo-EM map
Sample
  • Complex: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
    • Protein or peptide: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H4
    • DNA: DNA (192-MER)
    • DNA: DNA (192-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION
Keywordshelicase / chimera / complex / TRANSLOCASE
Function / homology
Function and homology information


chromosomal DNA methylation maintenance following DNA replication / DNA-mediated transformation / urogenital system development / retrotransposition / lymphocyte proliferation / pericentric heterochromatin formation / TGFBR3 expression / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway ...chromosomal DNA methylation maintenance following DNA replication / DNA-mediated transformation / urogenital system development / retrotransposition / lymphocyte proliferation / pericentric heterochromatin formation / TGFBR3 expression / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of gene expression via chromosomal CpG island methylation / negative regulation of intrinsic apoptotic signaling pathway / chromosome, centromeric region / pericentric heterochromatin / DNA helicase activity / cellular response to leukemia inhibitory factor / epigenetic regulation of gene expression / kidney development / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / DNA helicase / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / hydrolase activity / chromatin remodeling / protein heterodimerization activity / cell division / apoptotic process / chromatin binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site ...HELLS, N-terminal / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / : / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Helicase conserved C-terminal domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Histone H4 / Histone H2B 1.1 / Histone H3.2 / Histone H2A / Lymphoid-specific helicase / ATP-dependent DNA helicase DDM1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Xenopus laevis (African clawed frog) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsNartey W / Williams GJ
Funding support Canada, 1 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-04327 Canada
CitationJournal: To Be Published
Title: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
Authors: Nartey W / Williams GJ
History
DepositionApr 20, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40569.png

Downloads & links

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Map

FileDownload / File: emd_40569.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNon-sharpened cryo-EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.77 Å/pix.
x 448 pix.
= 344.96 Å		0.77 Å/pix.
x 448 pix.
= 344.96 Å		0.77 Å/pix.
x 448 pix.
= 344.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.043
Minimum - Maximum-0.19295526 - 0.38595298
Average (Standard dev.)0.000011510032 (±0.010576245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 344.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_40569_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened cryo-EM map

Fileemd_40569_additional_1.map
AnnotationSharpened cryo-EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map B

Fileemd_40569_half_map_1.map
AnnotationUnfiltered half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half-map A

Fileemd_40569_half_map_2.map
AnnotationUnfiltered half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome

EntireName: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
Components
  • Complex: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
    • Protein or peptide: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B 1.1
    • Protein or peptide: Histone H4
    • DNA: DNA (192-MER)
    • DNA: DNA (192-MER)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: BERYLLIUM TRIFLUORIDE ION

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Supramolecule #1: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome

SupramoleculeName: Cryo-EM complex of DDM1-HELLS chimera bound to the nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera

MacromoleculeName: ATP-dependent DNA helicase DDM1,Lymphoid-specific helicase chimera
type: protein_or_peptide / ID: 1
Details: This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis ...Details: This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag,This protein is a chimera of Arabidopsis thaliana DDM1 and Homo sapiens HELLS The first 3 amino acids (SNA) are a remnant of an expression tag
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 93.326195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SNAMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ...String:
SNAMVSLRSR KVIPASEMVS DGKTEKDASG DSPTSVLNEE ENCEEKSVTV VEEEILLAKN GDSSLISEAM AQEEEQLLKL REDEEKANN AGSAVAPNLN ETQFTKLDEL LTQTQLYSEF LLEKMEDITI NGIESESQKA EPEKTGRGRK RKAASQYNNT K AKRAVAAM ISRSKEDGET INSDLTEEET VIKLQNELCP LLTGGQLKSY QLKGVKWLIS LWQNGLNGIL ADQMGLGKTI QT IGFLSHL KGNGLDGPYL VIAPLSTLSN WFNEIARFTP SINAIIYHGD KNQRDELRRK HMPKTVGPKF PIVITSYEVA MND AKRILR HYPWKYVVID EGHRLKNHKC KLLRELKHLK MDNKLLLTGT PLQNNLSELW SLLNFILPDI FTSHDEFESW FDFS EKNKN EATKEEEEKR RAQVVSKLHG ILRPFILRRM KCDVELSLPR KKEIIMYATM TDHQKKFQEH LVNNTLEAHL GENAI RGIE LSPTGRPKRR TRKSINYSKI DDFPNELEKL ISQIQPEVDR ERAVVEVNIP VEQGWKGKLN NLVIQLRKNC NHPDLL QGQ IDGSYLYPPV EEIVGQCGKF RLLERLLVRL FANNHKVLIF SQWTKLLDIM DYYFSEKGFE VCRIDGSVKL DERRRQI KD FSDEKSSCSI FLLSTRAGGL GINLTAADTC ILYDSDWNPQ MDLQAMDRCH RIGQTKPVHV YRLSTAQSIE TRVLKRAY S KLKLEHVVIG QGQFHQERAK SSTPLEEEDI LALLKEDETA EDKLIQTDIS DADLDRLLDR SDLTITAPGE TQAAEAFPV KGPGWEVVLP SSGGMLSSLN S

UniProtKB: ATP-dependent DNA helicase DDM1, Lymphoid-specific helicase, ATP-dependent DNA helicase DDM1

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Macromolecule #2: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.435126 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVALFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 14.381696 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SNAMSGRGKQ GGKTRAKAKT RSSRAGLQFP VGRVHRLLRK GNYAERVGAG APVYLAAVLE YLTAEILELA GNAARDNKKT RIIPRHLQL AVRNDEELNK LLGRVTIAQG GVLPNIQSVL LPKKTESSKS AKSK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 12.276354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGGSENLYF Q

UniProtKB: Histone H4

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Macromolecule #6: DNA (192-MER)

MacromoleculeName: DNA (192-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.004613 KDa
SequenceString: (DG)(DA)(DA)(DA)(DA)(DC)(DC)(DT)(DG)(DT) (DA)(DC)(DT)(DT)(DC)(DC)(DA)(DA)(DT)(DC) (DC)(DA)(DA)(DT)(DA)(DG)(DG)(DC)(DC) (DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC) (DC)(DC)(DG)(DG)(DT)(DG) ...String:
(DG)(DA)(DA)(DA)(DA)(DC)(DC)(DT)(DG)(DT) (DA)(DC)(DT)(DT)(DC)(DC)(DA)(DA)(DT)(DC) (DC)(DA)(DA)(DT)(DA)(DG)(DG)(DC)(DC) (DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DG)(DA)(DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA)(DA) (DT)(DT)(DG)(DG)(DT)(DC)(DG) (DT)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG) (DC)(DA)(DC)(DC)(DG)(DC) (DT)(DT)(DA)(DA)(DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC) (DG)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DC)(DC)(DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG) (DC)(DC)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC) (DC)(DT)(DA) (DG)(DT)(DC)(DT)(DC)(DC)(DA)(DG)(DG)(DC) (DA)(DC)(DG)(DT)(DG)(DT)(DC) (DA)(DG) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DA)(DT) (DC)(DC)(DT)(DG)(DT)(DG)(DC)(DA) (DT) (DG)(DT)(DA)(DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG)

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Macromolecule #7: DNA (192-MER)

MacromoleculeName: DNA (192-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 59.546941 KDa
SequenceString: (DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG) (DC)(DC)(DT)(DG)(DG)(DA) ...String:
(DC)(DT)(DG)(DT)(DT)(DC)(DA)(DA)(DT)(DA) (DC)(DA)(DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG) (DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG) (DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT) (DC)(DC)(DC)(DC)(DT)(DT)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC) (DG)(DG)(DG)(DG)(DG)(DA) (DC)(DA)(DG)(DC)(DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DG)(DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT) (DA)(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG) (DC)(DC)(DT) (DC)(DG)(DG)(DC)(DA)(DC)(DC)(DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT)(DC)(DC) (DA)(DG) (DA)(DG)(DG)(DC)(DC)(DT)(DA)(DT)(DT)(DG) (DG)(DA)(DT)(DT)(DG)(DG)(DA)(DA) (DG) (DT)(DA)(DC)(DA)(DG)(DG)(DT)(DT)(DT)(DT) (DC)

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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #9: BERYLLIUM TRIFLUORIDE ION

MacromoleculeName: BERYLLIUM TRIFLUORIDE ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: BEF
Molecular weightTheoretical: 66.007 Da
Chemical component information

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7808 / Average exposure time: 4.95 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 84067
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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